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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.7

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Genome:
        hg19, 3137161264 bp
        Target:
        agilent5.bed (50390601 bp or 1.61% of the genome, 230418 regions, 124664 genes)

        Report generated on 2019-05-17, 19:50 based on data in:

        General Statistics

        Showing 166/166 rows and 16/32 columns.
        Sample NameReadsAlnRiPDupOn-trgUsableCovMean IS% Proper PairsVarsHomHetSNPIndelTs/Tv% GC
        Sample1
        1.8 M
        99.8%
        0.000%
        18.8%
        67.1%
        54.3%
        1.0
        183
        99.3%
        237284
        135
        220
        361
        31
        2.41
        43%
        Sample10
        0.5 M
        99.4%
        0.000%
        6.9%
        55.0%
        50.8%
        0.0
        272
        98.8%
        252802
        128
        214
        361
        16
        2.22
        41%
        Sample100
        1.1 M
        99.8%
        0.000%
        10.5%
        62.2%
        55.5%
        0.0
        246
        99.0%
        240062
        137
        221
        365
        22
        2.65
        45%
        Sample101
        2.2 M
        99.6%
        0.000%
        16.3%
        61.4%
        51.1%
        1.0
        264
        98.7%
        237223
        142
        223
        368
        23
        2.50
        46%
        Sample102
        2.1 M
        99.7%
        0.000%
        25.4%
        68.7%
        51.1%
        1.0
        174
        99.2%
        237333
        125
        230
        360
        20
        2.27
        44%
        Sample103
        1.6 M
        99.7%
        0.000%
        15.7%
        62.7%
        52.7%
        1.0
        229
        99.1%
        237706
        133
        188
        322
        22
        2.49
        44%
        Sample104
        1.7 M
        99.6%
        0.000%
        12.8%
        58.8%
        51.0%
        1.0
        233
        99.0%
        238491
        147
        224
        375
        28
        2.32
        45%
        Sample105
        2.2 M
        99.7%
        0.000%
        21.5%
        66.4%
        51.9%
        1.0
        201
        99.2%
        236829
        124
        245
        373
        26
        2.40
        44%
        Sample106
        2.1 M
        99.8%
        0.000%
        25.6%
        69.4%
        51.5%
        1.0
        170
        99.3%
        237171
        133
        231
        369
        28
        2.21
        44%
        Sample107
        2.8 M
        99.7%
        0.000%
        27.0%
        67.0%
        48.7%
        1.0
        186
        99.2%
        236527
        134
        225
        362
        21
        2.22
        44%
        Sample108
        2.4 M
        99.8%
        0.000%
        25.7%
        67.1%
        49.7%
        1.0
        190
        99.3%
        236637
        155
        214
        371
        22
        2.35
        44%
        Sample109
        2.2 M
        99.6%
        0.000%
        18.8%
        61.3%
        49.5%
        1.0
        267
        98.6%
        237337
        122
        243
        368
        31
        2.60
        47%
        Sample11
        2.1 M
        99.7%
        0.000%
        16.8%
        62.3%
        51.7%
        1.0
        250
        99.0%
        237239
        131
        228
        361
        26
        2.43
        46%
        Sample110
        2.5 M
        99.8%
        0.000%
        24.9%
        65.7%
        49.2%
        1.0
        196
        99.3%
        236501
        143
        221
        369
        25
        2.59
        44%
        Sample111
        2.3 M
        99.7%
        0.000%
        20.0%
        63.2%
        50.4%
        1.0
        230
        99.1%
        236959
        139
        215
        355
        32
        2.60
        44%
        Sample112
        1.9 M
        99.6%
        0.000%
        15.0%
        62.2%
        52.7%
        1.0
        258
        98.7%
        237503
        128
        206
        339
        20
        2.38
        46%
        Sample113
        1.1 M
        99.7%
        0.000%
        16.0%
        65.8%
        55.1%
        0.0
        190
        99.3%
        240402
        123
        210
        335
        26
        2.51
        42%
        Sample114
        1.7 M
        99.4%
        0.000%
        19.9%
        60.8%
        48.3%
        0.0
        208
        98.5%
        239344
        148
        206
        361
        27
        2.88
        42%
        Sample115
        0.7 M
        99.6%
        0.000%
        13.2%
        62.8%
        54.3%
        0.0
        179
        98.3%
        245691
        149
        208
        381
        25
        1.98
        41%
        Sample116
        0.9 M
        99.5%
        0.000%
        12.1%
        60.2%
        52.6%
        0.0
        218
        98.9%
        243324
        120
        218
        353
        29
        2.13
        42%
        Sample117
        1.0 M
        99.8%
        0.000%
        14.5%
        65.5%
        55.8%
        0.0
        205
        99.4%
        239702
        118
        210
        332
        19
        2.25
        43%
        Sample118
        2.3 M
        99.7%
        0.000%
        22.2%
        64.4%
        49.9%
        1.0
        220
        99.2%
        236881
        166
        215
        386
        24
        2.18
        44%
        Sample119
        2.6 M
        99.7%
        0.000%
        25.4%
        66.7%
        49.5%
        1.0
        196
        99.1%
        236658
        155
        218
        375
        29
        2.56
        44%
        Sample12
        1.4 M
        99.6%
        0.000%
        11.4%
        57.0%
        50.3%
        0.0
        246
        99.1%
        239123
        154
        219
        383
        21
        2.07
        43%
        Sample120
        0.8 M
        99.5%
        0.000%
        9.8%
        58.2%
        52.2%
        0.0
        222
        98.8%
        244950
        134
        196
        344
        24
        2.22
        41%
        Sample121
        2.9 M
        99.6%
        0.000%
        24.2%
        59.9%
        45.2%
        1.0
        224
        99.0%
        237573
        154
        236
        398
        28
        2.19
        44%
        Sample122
        2.4 M
        99.8%
        0.000%
        28.9%
        70.0%
        49.7%
        1.0
        161
        99.5%
        236784
        137
        242
        383
        23
        2.15
        43%
        Sample123
        2.2 M
        99.7%
        0.000%
        17.1%
        62.1%
        51.3%
        1.0
        248
        99.1%
        237070
        121
        270
        393
        26
        2.57
        46%
        Sample124
        2.7 M
        99.7%
        0.000%
        20.7%
        60.1%
        47.4%
        1.0
        208
        99.1%
        237400
        168
        220
        395
        35
        2.09
        43%
        Sample125
        2.8 M
        99.7%
        0.000%
        26.5%
        66.5%
        48.8%
        1.0
        198
        99.2%
        236368
        145
        210
        359
        30
        2.00
        44%
        Sample126
        2.1 M
        99.8%
        0.000%
        24.9%
        66.9%
        50.1%
        1.0
        181
        99.2%
        236919
        147
        232
        379
        26
        2.59
        43%
        Sample127
        1.5 M
        99.7%
        0.000%
        22.4%
        62.9%
        48.6%
        0.0
        173
        98.8%
        240152
        139
        224
        374
        22
        2.32
        42%
        Sample128
        2.6 M
        99.8%
        0.000%
        27.9%
        67.6%
        48.6%
        1.0
        181
        99.3%
        236442
        121
        207
        334
        20
        2.32
        44%
        Sample129
        1.8 M
        99.8%
        0.000%
        25.6%
        62.5%
        46.4%
        0.0
        179
        98.6%
        238956
        140
        223
        371
        24
        1.97
        42%
        Sample13
        1.6 M
        99.7%
        0.000%
        17.3%
        62.2%
        51.2%
        1.0
        237
        99.1%
        237354
        149
        207
        359
        28
        2.45
        44%
        Sample130
        3.2 M
        99.7%
        0.000%
        31.4%
        68.4%
        46.8%
        1.0
        175
        99.2%
        236411
        135
        229
        366
        23
        2.32
        44%
        Sample131
        1.6 M
        99.8%
        0.000%
        21.0%
        61.8%
        48.7%
        0.0
        174
        98.9%
        239815
        153
        219
        378
        29
        2.36
        42%
        Sample132
        2.7 M
        99.8%
        0.000%
        27.5%
        67.5%
        48.8%
        1.0
        182
        99.4%
        236360
        119
        238
        358
        26
        2.34
        44%
        Sample133
        0.9 M
        99.7%
        0.000%
        9.8%
        60.1%
        54.0%
        0.0
        257
        99.0%
        242037
        121
        234
        361
        30
        2.51
        43%
        Sample134
        2.4 M
        99.7%
        0.000%
        28.7%
        67.8%
        48.2%
        1.0
        174
        99.1%
        236819
        156
        222
        380
        27
        2.46
        43%
        Sample135
        0.7 M
        99.6%
        0.000%
        7.2%
        58.2%
        53.8%
        0.0
        284
        98.7%
        245897
        137
        209
        353
        22
        2.33
        44%
        Sample136
        2.0 M
        99.7%
        0.000%
        21.9%
        66.1%
        51.5%
        1.0
        202
        99.3%
        237140
        134
        225
        363
        24
        2.31
        44%
        Sample137
        1.5 M
        99.6%
        0.000%
        19.1%
        62.7%
        50.5%
        0.0
        169
        98.3%
        240582
        165
        228
        402
        32
        2.03
        42%
        Sample138
        2.1 M
        99.7%
        0.000%
        19.6%
        62.9%
        50.4%
        1.0
        175
        98.9%
        238343
        178
        211
        396
        33
        2.28
        43%
        Sample139
        0.9 M
        99.7%
        0.000%
        13.1%
        63.9%
        55.3%
        0.0
        213
        99.2%
        241992
        127
        216
        351
        19
        2.63
        41%
        Sample14
        1.4 M
        99.8%
        0.000%
        16.5%
        66.0%
        55.0%
        0.0
        194
        99.4%
        238523
        128
        220
        356
        23
        2.57
        43%
        Sample140
        1.3 M
        99.8%
        0.000%
        17.3%
        66.6%
        54.9%
        0.0
        187
        99.3%
        238575
        127
        231
        362
        23
        2.23
        43%
        Sample141
        3.0 M
        99.4%
        0.000%
        21.5%
        59.7%
        46.5%
        1.0
        230
        98.6%
        237555
        168
        223
        394
        21
        1.99
        44%
        Sample142
        1.1 M
        99.7%
        0.000%
        12.8%
        64.3%
        55.8%
        0.0
        215
        99.1%
        238898
        129
        226
        359
        23
        2.35
        43%
        Sample143
        2.4 M
        99.7%
        0.000%
        18.1%
        63.4%
        51.8%
        1.0
        235
        98.9%
        236814
        138
        217
        360
        24
        2.62
        46%
        Sample144
        2.0 M
        99.7%
        0.000%
        22.3%
        64.9%
        50.2%
        1.0
        201
        99.1%
        237255
        143
        200
        345
        27
        2.21
        44%
        Sample145
        1.5 M
        99.7%
        0.000%
        12.7%
        62.3%
        54.2%
        0.0
        239
        99.0%
        237998
        137
        216
        353
        24
        2.52
        45%
        Sample146
        0.4 M
        99.4%
        0.000%
        11.3%
        61.1%
        53.8%
        0.0
        173
        97.7%
        253917
        120
        225
        366
        20
        2.10
        40%
        Sample147
        1.9 M
        99.7%
        0.000%
        15.1%
        62.7%
        53.0%
        1.0
        241
        98.9%
        237312
        130
        220
        351
        23
        2.45
        45%
        Sample148
        3.5 M
        99.6%
        0.000%
        23.9%
        62.6%
        47.5%
        1.0
        234
        98.9%
        236497
        149
        216
        367
        31
        2.26
        45%
        Sample149
        2.3 M
        99.7%
        0.000%
        18.8%
        62.7%
        50.7%
        1.0
        233
        99.0%
        236830
        155
        190
        348
        26
        2.12
        45%
        Sample15
        2.2 M
        99.6%
        0.000%
        16.7%
        61.7%
        51.2%
        1.0
        259
        98.6%
        237238
        135
        234
        371
        32
        2.48
        47%
        Sample150
        1.6 M
        99.6%
        0.000%
        14.3%
        61.3%
        52.3%
        1.0
        263
        98.7%
        238444
        120
        247
        371
        20
        2.37
        47%
        Sample151
        0.9 M
        99.8%
        0.000%
        9.8%
        63.4%
        57.0%
        0.0
        226
        99.3%
        240806
        126
        162
        290
        18
        2.67
        42%
        Sample152
        2.3 M
        99.7%
        0.000%
        17.0%
        62.2%
        51.5%
        1.0
        246
        98.9%
        236776
        129
        225
        358
        22
        2.19
        45%
        Sample153
        1.2 M
        99.7%
        0.000%
        12.0%
        61.8%
        54.2%
        0.0
        255
        98.9%
        239428
        137
        232
        371
        30
        2.72
        45%
        Sample154
        1.7 M
        99.7%
        0.000%
        15.3%
        62.7%
        52.9%
        1.0
        252
        98.6%
        238403
        152
        241
        398
        26
        2.35
        47%
        Sample155
        1.5 M
        99.5%
        0.000%
        14.9%
        60.8%
        51.4%
        0.0
        272
        98.4%
        239020
        130
        229
        366
        32
        2.44
        47%
        Sample156
        2.0 M
        99.7%
        0.000%
        19.5%
        62.0%
        49.7%
        1.0
        194
        99.0%
        238163
        180
        210
        393
        32
        1.99
        43%
        Sample157
        2.2 M
        99.7%
        0.000%
        24.5%
        67.4%
        50.7%
        1.0
        184
        99.2%
        236899
        128
        209
        341
        26
        2.25
        44%
        Sample158
        1.0 M
        99.7%
        0.000%
        10.3%
        62.1%
        55.5%
        0.0
        240
        99.1%
        240421
        137
        168
        311
        24
        2.49
        43%
        Sample159
        1.4 M
        99.6%
        0.000%
        29.4%
        62.2%
        43.7%
        0.0
        169
        97.4%
        241842
        163
        198
        377
        25
        2.02
        42%
        Sample16
        2.2 M
        99.7%
        0.000%
        16.8%
        62.2%
        51.5%
        1.0
        250
        98.8%
        237083
        127
        216
        344
        18
        2.41
        46%
        Sample160
        1.4 M
        99.8%
        0.000%
        19.0%
        67.9%
        54.9%
        0.0
        181
        99.3%
        238404
        115
        240
        357
        28
        2.21
        43%
        Sample161
        2.5 M
        99.5%
        0.000%
        19.6%
        60.7%
        48.5%
        1.0
        264
        98.6%
        236958
        138
        259
        401
        22
        2.38
        47%
        Sample162
        2.0 M
        99.7%
        0.000%
        19.4%
        63.4%
        50.9%
        1.0
        227
        99.2%
        237193
        141
        248
        395
        24
        2.44
        44%
        Sample163
        1.1 M
        99.7%
        0.000%
        14.6%
        65.1%
        55.4%
        0.0
        204
        99.2%
        239696
        123
        215
        347
        25
        2.25
        42%
        Sample164
        2.1 M
        99.7%
        0.000%
        21.3%
        65.1%
        51.1%
        1.0
        197
        99.3%
        237051
        164
        220
        390
        19
        2.40
        43%
        Sample165
        1.5 M
        99.7%
        0.000%
        19.0%
        63.7%
        51.4%
        0.0
        158
        98.3%
        240636
        174
        207
        387
        26
        2.12
        42%
        Sample166
        1.5 M
        99.7%
        0.000%
        28.5%
        62.1%
        44.2%
        0.0
        187
        98.0%
        241059
        151
        216
        377
        28
        2.64
        43%
        Sample17
        1.2 M
        99.6%
        0.000%
        11.7%
        60.8%
        53.4%
        0.0
        270
        98.6%
        239090
        133
        182
        322
        21
        2.76
        45%
        Sample18
        1.0 M
        99.6%
        0.000%
        10.3%
        60.2%
        53.8%
        0.0
        266
        98.8%
        240234
        129
        195
        327
        23
        2.59
        45%
        Sample19
        1.7 M
        99.7%
        0.000%
        19.8%
        65.9%
        52.6%
        1.0
        202
        99.2%
        237293
        109
        239
        351
        24
        2.25
        44%
        Sample2
        0.7 M
        99.6%
        0.000%
        8.8%
        62.2%
        56.4%
        0.0
        176
        98.5%
        246401
        121
        253
        385
        33
        2.27
        41%
        Sample20
        0.7 M
        99.6%
        0.000%
        15.0%
        63.3%
        53.5%
        0.0
        160
        97.5%
        246572
        140
        181
        340
        27
        2.03
        41%
        Sample21
        0.4 M
        99.4%
        0.000%
        10.0%
        61.9%
        55.3%
        0.0
        189
        97.9%
        255384
        124
        201
        345
        20
        2.56
        39%
        Sample22
        1.8 M
        99.8%
        0.000%
        17.6%
        65.8%
        54.1%
        1.0
        200
        99.2%
        237024
        107
        248
        357
        19
        2.57
        44%
        Sample23
        2.1 M
        99.5%
        0.000%
        16.1%
        62.3%
        52.0%
        1.0
        256
        98.6%
        237378
        149
        221
        372
        27
        2.44
        46%
        Sample24
        2.3 M
        99.8%
        0.000%
        24.0%
        66.7%
        50.5%
        1.0
        182
        99.3%
        236661
        130
        202
        334
        21
        2.13
        43%
        Sample25
        2.7 M
        99.7%
        0.000%
        26.2%
        66.7%
        49.0%
        1.0
        192
        99.0%
        236698
        128
        234
        365
        23
        2.35
        44%
        Sample26
        3.3 M
        99.6%
        0.000%
        26.8%
        63.8%
        46.5%
        1.0
        219
        98.9%
        236722
        148
        206
        355
        31
        2.39
        44%
        Sample27
        2.5 M
        99.7%
        0.000%
        18.5%
        59.5%
        48.3%
        1.0
        271
        99.0%
        236888
        134
        242
        380
        24
        2.47
        46%
        Sample28
        2.6 M
        99.7%
        0.000%
        29.1%
        67.5%
        47.7%
        1.0
        166
        99.1%
        236993
        141
        227
        370
        26
        2.59
        43%
        Sample29
        2.0 M
        99.7%
        0.000%
        17.4%
        63.4%
        52.2%
        1.0
        235
        99.0%
        237317
        129
        217
        349
        23
        2.58
        46%
        Sample3
        0.9 M
        99.5%
        0.000%
        13.8%
        62.2%
        53.3%
        0.0
        164
        97.7%
        243801
        150
        207
        366
        22
        2.16
        42%
        Sample30
        2.1 M
        99.7%
        0.000%
        19.2%
        60.9%
        49.0%
        1.0
        215
        99.3%
        237746
        151
        195
        352
        28
        1.88
        43%
        Sample31
        2.7 M
        99.6%
        0.000%
        26.4%
        66.4%
        48.6%
        1.0
        193
        99.0%
        236531
        141
        234
        377
        29
        2.29
        44%
        Sample32
        1.5 M
        99.8%
        0.000%
        19.6%
        67.8%
        54.4%
        0.0
        178
        99.4%
        238127
        154
        207
        363
        19
        2.47
        43%
        Sample33
        1.0 M
        99.6%
        0.000%
        12.9%
        61.1%
        53.0%
        0.0
        198
        99.0%
        242497
        166
        209
        391
        27
        2.33
        42%
        Sample34
        2.3 M
        99.8%
        0.000%
        27.5%
        68.9%
        49.8%
        1.0
        168
        99.5%
        236785
        142
        250
        394
        20
        2.28
        44%
        Sample35
        2.6 M
        99.8%
        0.000%
        24.6%
        66.5%
        50.0%
        1.0
        200
        99.3%
        236477
        150
        203
        358
        19
        2.26
        44%
        Sample36
        1.8 M
        99.8%
        0.000%
        18.2%
        66.0%
        53.9%
        1.0
        211
        99.2%
        237325
        121
        254
        382
        26
        2.23
        45%
        Sample37
        1.4 M
        99.7%
        0.000%
        16.2%
        66.5%
        55.6%
        0.0
        189
        99.1%
        238068
        120
        223
        346
        29
        2.41
        44%
        Sample38
        2.0 M
        99.8%
        0.000%
        22.2%
        67.2%
        52.1%
        1.0
        199
        99.3%
        236796
        125
        225
        355
        15
        2.59
        45%
        Sample39
        1.2 M
        99.7%
        0.000%
        11.5%
        60.6%
        53.5%
        0.0
        252
        99.0%
        239387
        132
        228
        363
        28
        2.18
        45%
        Sample4
        1.8 M
        99.8%
        0.000%
        15.4%
        63.4%
        53.5%
        1.0
        222
        99.3%
        237134
        128
        240
        373
        26
        2.84
        44%
        Sample40
        1.9 M
        99.8%
        0.000%
        16.0%
        64.1%
        53.7%
        1.0
        221
        99.3%
        236683
        136
        197
        336
        18
        2.22
        44%
        Sample41
        1.3 M
        99.8%
        0.000%
        16.1%
        64.9%
        54.3%
        0.0
        207
        99.4%
        238242
        126
        232
        362
        27
        2.72
        43%
        Sample42
        2.8 M
        99.7%
        0.000%
        25.6%
        65.7%
        48.7%
        1.0
        206
        99.0%
        236699
        134
        239
        376
        26
        2.27
        44%
        Sample43
        0.7 M
        99.6%
        0.000%
        10.6%
        62.4%
        55.6%
        0.0
        236
        99.1%
        244559
        106
        233
        342
        24
        2.36
        42%
        Sample44
        2.5 M
        99.8%
        0.000%
        23.9%
        64.7%
        49.0%
        1.0
        221
        99.2%
        236539
        130
        237
        367
        19
        2.54
        45%
        Sample45
        4.0 M
        99.6%
        0.000%
        32.2%
        64.6%
        43.6%
        2.0
        207
        98.9%
        236381
        130
        237
        374
        22
        2.29
        44%
        Sample46
        0.9 M
        99.7%
        0.000%
        13.4%
        64.7%
        55.8%
        0.0
        217
        99.3%
        240715
        126
        197
        327
        23
        2.51
        42%
        Sample47
        2.6 M
        99.6%
        0.000%
        24.6%
        65.3%
        49.1%
        1.0
        212
        99.0%
        236491
        139
        205
        346
        23
        2.11
        45%
        Sample48
        2.5 M
        99.8%
        0.000%
        25.5%
        66.0%
        49.1%
        1.0
        189
        99.3%
        236714
        165
        219
        386
        31
        2.54
        44%
        Sample49
        1.2 M
        99.6%
        0.000%
        18.1%
        62.4%
        50.8%
        0.0
        170
        98.4%
        242785
        136
        215
        360
        17
        1.98
        42%
        Sample5
        1.1 M
        99.7%
        0.000%
        13.4%
        66.1%
        57.1%
        0.0
        192
        99.2%
        239411
        150
        204
        358
        23
        2.21
        43%
        Sample50
        1.9 M
        99.7%
        0.000%
        16.1%
        62.5%
        52.2%
        1.0
        248
        98.8%
        237718
        140
        236
        379
        24
        2.75
        47%
        Sample51
        1.1 M
        99.6%
        0.000%
        15.3%
        64.5%
        54.3%
        0.0
        205
        99.0%
        239702
        119
        206
        331
        23
        2.12
        42%
        Sample52
        2.1 M
        99.7%
        0.000%
        23.4%
        66.3%
        50.6%
        1.0
        187
        99.3%
        237063
        137
        211
        349
        25
        2.60
        43%
        Sample53
        2.0 M
        99.8%
        0.000%
        22.8%
        65.8%
        50.7%
        1.0
        205
        99.3%
        236778
        130
        234
        366
        25
        2.68
        44%
        Sample54
        1.7 M
        99.7%
        0.000%
        14.3%
        61.8%
        52.8%
        1.0
        244
        99.0%
        238084
        145
        221
        370
        30
        2.59
        45%
        Sample55
        2.0 M
        99.8%
        0.000%
        25.2%
        69.4%
        51.7%
        1.0
        167
        99.2%
        237509
        132
        235
        370
        25
        2.47
        43%
        Sample56
        1.4 M
        99.3%
        0.000%
        14.7%
        61.1%
        51.7%
        0.0
        200
        98.3%
        240526
        162
        191
        364
        21
        2.17
        42%
        Sample57
        1.1 M
        99.6%
        0.000%
        11.2%
        60.5%
        53.5%
        0.0
        199
        98.9%
        241650
        140
        197
        353
        24
        2.10
        42%
        Sample58
        2.2 M
        99.7%
        0.000%
        19.4%
        61.6%
        49.5%
        1.0
        184
        98.9%
        238231
        176
        229
        408
        37
        2.06
        42%
        Sample59
        2.3 M
        99.7%
        0.000%
        22.1%
        60.8%
        47.2%
        1.0
        227
        99.1%
        237782
        167
        232
        404
        32
        2.19
        44%
        Sample6
        1.7 M
        99.7%
        0.000%
        16.1%
        58.6%
        49.0%
        1.0
        231
        99.1%
        238379
        167
        235
        421
        33
        2.21
        43%
        Sample60
        2.8 M
        99.7%
        0.000%
        23.6%
        62.3%
        47.5%
        1.0
        238
        99.2%
        236584
        153
        215
        373
        20
        2.07
        45%
        Sample61
        1.8 M
        99.7%
        0.000%
        20.3%
        60.7%
        48.2%
        1.0
        208
        99.2%
        238410
        144
        226
        378
        26
        2.17
        43%
        Sample62
        3.0 M
        99.8%
        0.000%
        25.4%
        64.5%
        48.0%
        1.0
        217
        99.3%
        236328
        137
        223
        365
        29
        2.17
        44%
        Sample63
        0.6 M
        99.6%
        0.000%
        7.1%
        58.9%
        54.5%
        0.0
        218
        99.1%
        249848
        110
        273
        405
        26
        2.13
        40%
        Sample64
        1.2 M
        99.5%
        0.000%
        29.0%
        61.9%
        43.7%
        0.0
        170
        97.6%
        243451
        134
        230
        380
        24
        2.24
        43%
        Sample65
        1.2 M
        99.7%
        0.000%
        11.3%
        63.0%
        55.7%
        0.0
        240
        99.0%
        238564
        135
        203
        341
        21
        2.70
        45%
        Sample66
        1.3 M
        99.7%
        0.000%
        12.6%
        61.4%
        53.4%
        0.0
        265
        98.7%
        238917
        123
        217
        344
        27
        2.34
        46%
        Sample67
        1.3 M
        99.7%
        0.000%
        13.2%
        61.0%
        52.8%
        0.0
        260
        98.8%
        238987
        137
        216
        354
        25
        2.51
        46%
        Sample68
        1.2 M
        99.6%
        0.000%
        16.9%
        60.5%
        50.1%
        0.0
        205
        98.9%
        240322
        141
        233
        391
        24
        2.23
        42%
        Sample69
        1.9 M
        99.6%
        0.000%
        27.0%
        61.8%
        44.8%
        0.0
        193
        97.9%
        239808
        164
        241
        415
        23
        2.04
        43%
        Sample7
        2.6 M
        99.6%
        0.000%
        26.1%
        64.8%
        47.7%
        1.0
        215
        99.0%
        236628
        127
        210
        341
        30
        2.48
        44%
        Sample70
        0.4 M
        99.5%
        0.000%
        13.0%
        63.1%
        54.5%
        0.0
        159
        96.9%
        253755
        110
        224
        357
        28
        2.04
        41%
        Sample71
        2.1 M
        99.8%
        0.000%
        21.8%
        65.6%
        51.1%
        1.0
        206
        99.2%
        236877
        142
        231
        374
        28
        2.39
        45%
        Sample72
        1.5 M
        99.7%
        0.000%
        12.8%
        62.6%
        54.4%
        1.0
        243
        99.1%
        238115
        126
        211
        338
        24
        2.38
        45%
        Sample73
        2.5 M
        99.8%
        0.000%
        31.9%
        69.8%
        47.4%
        1.0
        162
        99.3%
        236744
        109
        242
        356
        23
        2.37
        43%
        Sample74
        1.7 M
        99.8%
        0.000%
        18.4%
        64.3%
        52.3%
        1.0
        213
        99.3%
        237259
        121
        238
        361
        23
        2.62
        43%
        Sample75
        1.5 M
        99.6%
        0.000%
        13.0%
        62.1%
        53.7%
        0.0
        246
        98.9%
        238132
        122
        215
        341
        27
        2.44
        44%
        Sample76
        2.5 M
        99.5%
        0.000%
        28.5%
        61.4%
        43.7%
        1.0
        210
        98.6%
        238204
        152
        223
        384
        33
        1.92
        43%
        Sample77
        1.2 M
        99.6%
        0.000%
        12.7%
        62.2%
        54.0%
        0.0
        263
        98.6%
        240339
        131
        219
        352
        23
        2.58
        47%
        Sample78
        1.9 M
        99.6%
        0.000%
        25.4%
        61.6%
        45.8%
        0.0
        180
        98.5%
        239150
        161
        236
        410
        31
        2.02
        42%
        Sample79
        2.4 M
        99.8%
        0.000%
        30.1%
        69.7%
        48.6%
        1.0
        164
        99.2%
        236942
        126
        237
        364
        26
        2.26
        43%
        Sample8
        2.3 M
        99.7%
        0.000%
        18.6%
        63.5%
        51.5%
        1.0
        234
        99.0%
        237157
        141
        255
        401
        23
        2.18
        46%
        Sample80
        1.9 M
        99.8%
        0.000%
        23.4%
        68.3%
        52.2%
        1.0
        182
        99.3%
        237387
        128
        213
        345
        30
        2.15
        44%
        Sample81
        1.8 M
        99.6%
        0.000%
        29.0%
        62.1%
        43.9%
        0.0
        179
        97.7%
        240252
        156
        229
        395
        30
        2.34
        42%
        Sample82
        1.8 M
        99.6%
        0.000%
        19.0%
        59.3%
        47.8%
        1.0
        228
        98.9%
        238459
        144
        259
        412
        27
        2.18
        43%
        Sample83
        0.6 M
        99.4%
        0.000%
        16.6%
        62.7%
        51.9%
        0.0
        173
        97.3%
        249771
        154
        214
        388
        21
        2.11
        42%
        Sample84
        2.6 M
        99.8%
        0.000%
        28.7%
        68.3%
        48.5%
        1.0
        171
        99.3%
        236736
        149
        220
        373
        27
        2.30
        43%
        Sample85
        2.5 M
        99.7%
        0.000%
        27.2%
        66.7%
        48.4%
        1.0
        194
        99.2%
        236636
        122
        246
        375
        27
        2.46
        44%
        Sample86
        0.9 M
        99.7%
        0.000%
        10.0%
        64.5%
        57.8%
        0.0
        218
        99.1%
        240422
        122
        226
        352
        24
        2.71
        43%
        Sample87
        1.6 M
        99.8%
        0.000%
        17.6%
        64.8%
        53.2%
        1.0
        213
        99.3%
        237429
        133
        212
        350
        26
        2.28
        43%
        Sample88
        2.3 M
        99.8%
        0.000%
        21.7%
        60.6%
        47.3%
        1.0
        222
        99.3%
        237623
        161
        213
        379
        20
        2.12
        43%
        Sample89
        2.2 M
        99.8%
        0.000%
        28.0%
        69.8%
        50.2%
        1.0
        156
        99.4%
        237177
        137
        191
        331
        27
        2.31
        43%
        Sample9
        0.8 M
        99.6%
        0.000%
        15.1%
        60.8%
        51.3%
        0.0
        199
        99.0%
        244420
        129
        234
        382
        23
        2.17
        41%
        Sample90
        1.5 M
        99.8%
        0.000%
        15.1%
        65.6%
        55.5%
        1.0
        206
        99.3%
        237455
        125
        226
        352
        19
        2.41
        43%
        Sample91
        0.7 M
        99.7%
        0.000%
        8.3%
        62.3%
        56.9%
        0.0
        237
        99.1%
        243426
        112
        223
        339
        17
        2.43
        42%
        Sample92
        2.7 M
        99.7%
        0.000%
        20.6%
        63.8%
        50.5%
        1.0
        223
        99.0%
        236647
        121
        240
        363
        25
        2.24
        44%
        Sample93
        1.2 M
        99.6%
        0.000%
        20.0%
        62.2%
        49.5%
        0.0
        173
        98.5%
        242473
        147
        208
        370
        25
        2.10
        42%
        Sample94
        1.3 M
        99.7%
        0.000%
        10.5%
        60.4%
        53.8%
        0.0
        262
        98.9%
        239022
        134
        231
        366
        32
        2.53
        44%
        Sample95
        0.6 M
        99.6%
        0.000%
        10.0%
        59.8%
        53.5%
        0.0
        197
        98.8%
        247752
        123
        221
        359
        33
        2.32
        41%
        Sample96
        0.8 M
        99.4%
        0.000%
        8.4%
        57.2%
        52.1%
        0.0
        237
        98.9%
        243813
        141
        214
        373
        28
        2.12
        42%
        Sample97
        1.1 M
        99.8%
        0.000%
        14.8%
        65.3%
        55.5%
        0.0
        201
        99.3%
        240395
        122
        209
        333
        25
        2.46
        42%
        Sample98
        1.9 M
        99.8%
        0.000%
        23.8%
        67.8%
        51.5%
        1.0
        165
        99.3%
        237702
        140
        230
        375
        30
        2.23
        43%
        Sample99
        2.0 M
        99.7%
        0.000%
        20.8%
        65.6%
        51.8%
        1.0
        208
        99.1%
        236911
        141
        206
        354
        27
        2.42
        45%

        Samtools

        Samtools is a suite of programs for interacting with high-throughput sequencing data.

        Percent Mapped

        Alignment metrics from samtools stats; mapped vs. unmapped reads.

        For a set of samples that have come from the same multiplexed library, similar numbers of reads for each sample are expected. Large differences in numbers might indicate issues during the library preparation process. Whilst large differences in read numbers may be controlled for in downstream processings (e.g. read count normalisation), you may wish to consider whether the read depths achieved have fallen below recommended levels depending on the applications.

        Low alignment rates could indicate contamination of samples (e.g. adapter sequences), low sequencing quality or other artefacts. These can be further investigated in the sequence level QC (e.g. from FastQC).

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Alignment metrics

        This module parses the output from samtools stats. All numbers in millions.

        loading..

        XY counts

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Mapped reads per contig

        The samtools idxstats tool counts the number of mapped reads per chromosome / contig. Chromosomes with < 0.1% of the total aligned reads are omitted from this plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Bcftools

        Bcftools contains utilities for variant calling and manipulating VCFs and BCFs.

        Bcftools Stats

        Showing 166/166 rows and 6/7 columns.
        Sample NameVarsHomHetSNPIndelTs/Tv
        Sample1
        237284
        135
        220
        361
        31
        2.41
        Sample10
        252802
        128
        214
        361
        16
        2.22
        Sample100
        240062
        137
        221
        365
        22
        2.65
        Sample101
        237223
        142
        223
        368
        23
        2.50
        Sample102
        237333
        125
        230
        360
        20
        2.27
        Sample103
        237706
        133
        188
        322
        22
        2.49
        Sample104
        238491
        147
        224
        375
        28
        2.32
        Sample105
        236829
        124
        245
        373
        26
        2.40
        Sample106
        237171
        133
        231
        369
        28
        2.21
        Sample107
        236527
        134
        225
        362
        21
        2.22
        Sample108
        236637
        155
        214
        371
        22
        2.35
        Sample109
        237337
        122
        243
        368
        31
        2.60
        Sample11
        237239
        131
        228
        361
        26
        2.43
        Sample110
        236501
        143
        221
        369
        25
        2.59
        Sample111
        236959
        139
        215
        355
        32
        2.60
        Sample112
        237503
        128
        206
        339
        20
        2.38
        Sample113
        240402
        123
        210
        335
        26
        2.51
        Sample114
        239344
        148
        206
        361
        27
        2.88
        Sample115
        245691
        149
        208
        381
        25
        1.98
        Sample116
        243324
        120
        218
        353
        29
        2.13
        Sample117
        239702
        118
        210
        332
        19
        2.25
        Sample118
        236881
        166
        215
        386
        24
        2.18
        Sample119
        236658
        155
        218
        375
        29
        2.56
        Sample12
        239123
        154
        219
        383
        21
        2.07
        Sample120
        244950
        134
        196
        344
        24
        2.22
        Sample121
        237573
        154
        236
        398
        28
        2.19
        Sample122
        236784
        137
        242
        383
        23
        2.15
        Sample123
        237070
        121
        270
        393
        26
        2.57
        Sample124
        237400
        168
        220
        395
        35
        2.09
        Sample125
        236368
        145
        210
        359
        30
        2.00
        Sample126
        236919
        147
        232
        379
        26
        2.59
        Sample127
        240152
        139
        224
        374
        22
        2.32
        Sample128
        236442
        121
        207
        334
        20
        2.32
        Sample129
        238956
        140
        223
        371
        24
        1.97
        Sample13
        237354
        149
        207
        359
        28
        2.45
        Sample130
        236411
        135
        229
        366
        23
        2.32
        Sample131
        239815
        153
        219
        378
        29
        2.36
        Sample132
        236360
        119
        238
        358
        26
        2.34
        Sample133
        242037
        121
        234
        361
        30
        2.51
        Sample134
        236819
        156
        222
        380
        27
        2.46
        Sample135
        245897
        137
        209
        353
        22
        2.33
        Sample136
        237140
        134
        225
        363
        24
        2.31
        Sample137
        240582
        165
        228
        402
        32
        2.03
        Sample138
        238343
        178
        211
        396
        33
        2.28
        Sample139
        241992
        127
        216
        351
        19
        2.63
        Sample14
        238523
        128
        220
        356
        23
        2.57
        Sample140
        238575
        127
        231
        362
        23
        2.23
        Sample141
        237555
        168
        223
        394
        21
        1.99
        Sample142
        238898
        129
        226
        359
        23
        2.35
        Sample143
        236814
        138
        217
        360
        24
        2.62
        Sample144
        237255
        143
        200
        345
        27
        2.21
        Sample145
        237998
        137
        216
        353
        24
        2.52
        Sample146
        253917
        120
        225
        366
        20
        2.10
        Sample147
        237312
        130
        220
        351
        23
        2.45
        Sample148
        236497
        149
        216
        367
        31
        2.26
        Sample149
        236830
        155
        190
        348
        26
        2.12
        Sample15
        237238
        135
        234
        371
        32
        2.48
        Sample150
        238444
        120
        247
        371
        20
        2.37
        Sample151
        240806
        126
        162
        290
        18
        2.67
        Sample152
        236776
        129
        225
        358
        22
        2.19
        Sample153
        239428
        137
        232
        371
        30
        2.72
        Sample154
        238403
        152
        241
        398
        26
        2.35
        Sample155
        239020
        130
        229
        366
        32
        2.44
        Sample156
        238163
        180
        210
        393
        32
        1.99
        Sample157
        236899
        128
        209
        341
        26
        2.25
        Sample158
        240421
        137
        168
        311
        24
        2.49
        Sample159
        241842
        163
        198
        377
        25
        2.02
        Sample16
        237083
        127
        216
        344
        18
        2.41
        Sample160
        238404
        115
        240
        357
        28
        2.21
        Sample161
        236958
        138
        259
        401
        22
        2.38
        Sample162
        237193
        141
        248
        395
        24
        2.44
        Sample163
        239696
        123
        215
        347
        25
        2.25
        Sample164
        237051
        164
        220
        390
        19
        2.40
        Sample165
        240636
        174
        207
        387
        26
        2.12
        Sample166
        241059
        151
        216
        377
        28
        2.64
        Sample17
        239090
        133
        182
        322
        21
        2.76
        Sample18
        240234
        129
        195
        327
        23
        2.59
        Sample19
        237293
        109
        239
        351
        24
        2.25
        Sample2
        246401
        121
        253
        385
        33
        2.27
        Sample20
        246572
        140
        181
        340
        27
        2.03
        Sample21
        255384
        124
        201
        345
        20
        2.56
        Sample22
        237024
        107
        248
        357
        19
        2.57
        Sample23
        237378
        149
        221
        372
        27
        2.44
        Sample24
        236661
        130
        202
        334
        21
        2.13
        Sample25
        236698
        128
        234
        365
        23
        2.35
        Sample26
        236722
        148
        206
        355
        31
        2.39
        Sample27
        236888
        134
        242
        380
        24
        2.47
        Sample28
        236993
        141
        227
        370
        26
        2.59
        Sample29
        237317
        129
        217
        349
        23
        2.58
        Sample3
        243801
        150
        207
        366
        22
        2.16
        Sample30
        237746
        151
        195
        352
        28
        1.88
        Sample31
        236531
        141
        234
        377
        29
        2.29
        Sample32
        238127
        154
        207
        363
        19
        2.47
        Sample33
        242497
        166
        209
        391
        27
        2.33
        Sample34
        236785
        142
        250
        394
        20
        2.28
        Sample35
        236477
        150
        203
        358
        19
        2.26
        Sample36
        237325
        121
        254
        382
        26
        2.23
        Sample37
        238068
        120
        223
        346
        29
        2.41
        Sample38
        236796
        125
        225
        355
        15
        2.59
        Sample39
        239387
        132
        228
        363
        28
        2.18
        Sample4
        237134
        128
        240
        373
        26
        2.84
        Sample40
        236683
        136
        197
        336
        18
        2.22
        Sample41
        238242
        126
        232
        362
        27
        2.72
        Sample42
        236699
        134
        239
        376
        26
        2.27
        Sample43
        244559
        106
        233
        342
        24
        2.36
        Sample44
        236539
        130
        237
        367
        19
        2.54
        Sample45
        236381
        130
        237
        374
        22
        2.29
        Sample46
        240715
        126
        197
        327
        23
        2.51
        Sample47
        236491
        139
        205
        346
        23
        2.11
        Sample48
        236714
        165
        219
        386
        31
        2.54
        Sample49
        242785
        136
        215
        360
        17
        1.98
        Sample5
        239411
        150
        204
        358
        23
        2.21
        Sample50
        237718
        140
        236
        379
        24
        2.75
        Sample51
        239702
        119
        206
        331
        23
        2.12
        Sample52
        237063
        137
        211
        349
        25
        2.60
        Sample53
        236778
        130
        234
        366
        25
        2.68
        Sample54
        238084
        145
        221
        370
        30
        2.59
        Sample55
        237509
        132
        235
        370
        25
        2.47
        Sample56
        240526
        162
        191
        364
        21
        2.17
        Sample57
        241650
        140
        197
        353
        24
        2.10
        Sample58
        238231
        176
        229
        408
        37
        2.06
        Sample59
        237782
        167
        232
        404
        32
        2.19
        Sample6
        238379
        167
        235
        421
        33
        2.21
        Sample60
        236584
        153
        215
        373
        20
        2.07
        Sample61
        238410
        144
        226
        378
        26
        2.17
        Sample62
        236328
        137
        223
        365
        29
        2.17
        Sample63
        249848
        110
        273
        405
        26
        2.13
        Sample64
        243451
        134
        230
        380
        24
        2.24
        Sample65
        238564
        135
        203
        341
        21
        2.70
        Sample66
        238917
        123
        217
        344
        27
        2.34
        Sample67
        238987
        137
        216
        354
        25
        2.51
        Sample68
        240322
        141
        233
        391
        24
        2.23
        Sample69
        239808
        164
        241
        415
        23
        2.04
        Sample7
        236628
        127
        210
        341
        30
        2.48
        Sample70
        253755
        110
        224
        357
        28
        2.04
        Sample71
        236877
        142
        231
        374
        28
        2.39
        Sample72
        238115
        126
        211
        338
        24
        2.38
        Sample73
        236744
        109
        242
        356
        23
        2.37
        Sample74
        237259
        121
        238
        361
        23
        2.62
        Sample75
        238132
        122
        215
        341
        27
        2.44
        Sample76
        238204
        152
        223
        384
        33
        1.92
        Sample77
        240339
        131
        219
        352
        23
        2.58
        Sample78
        239150
        161
        236
        410
        31
        2.02
        Sample79
        236942
        126
        237
        364
        26
        2.26
        Sample8
        237157
        141
        255
        401
        23
        2.18
        Sample80
        237387
        128
        213
        345
        30
        2.15
        Sample81
        240252
        156
        229
        395
        30
        2.34
        Sample82
        238459
        144
        259
        412
        27
        2.18
        Sample83
        249771
        154
        214
        388
        21
        2.11
        Sample84
        236736
        149
        220
        373
        27
        2.30
        Sample85
        236636
        122
        246
        375
        27
        2.46
        Sample86
        240422
        122
        226
        352
        24
        2.71
        Sample87
        237429
        133
        212
        350
        26
        2.28
        Sample88
        237623
        161
        213
        379
        20
        2.12
        Sample89
        237177
        137
        191
        331
        27
        2.31
        Sample9
        244420
        129
        234
        382
        23
        2.17
        Sample90
        237455
        125
        226
        352
        19
        2.41
        Sample91
        243426
        112
        223
        339
        17
        2.43
        Sample92
        236647
        121
        240
        363
        25
        2.24
        Sample93
        242473
        147
        208
        370
        25
        2.10
        Sample94
        239022
        134
        231
        366
        32
        2.53
        Sample95
        247752
        123
        221
        359
        33
        2.32
        Sample96
        243813
        141
        214
        373
        28
        2.12
        Sample97
        240395
        122
        209
        333
        25
        2.46
        Sample98
        237702
        140
        230
        375
        30
        2.23
        Sample99
        236911
        141
        206
        354
        27
        2.42

        Variant Substitution Types

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Variant Quality

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Indel Distribution

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Variant depths

        Read depth support distribution for called variants

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        SnpEff

        SnpEff is a genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes).

        Variants by Genomic Region

        The stacked bar plot shows locations of detected variants in the genome and the number of variants for each location.

        The upstream and downstream interval size to detect these genomic regions is 5000bp by default.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Variant Effects by Impact

        The stacked bar plot shows the putative impact of detected variants and the number of variants for each impact.

        There are four levels of impacts predicted by SnpEff:

        • High: High impact (like stop codon)
        • Moderate: Middle impact (like same type of amino acid substitution)
        • Low: Low impact (ie silence mutation)
        • Modifier: No impact

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Variant Effects by Class

        The stacked bar plot shows the effect of variants at protein level and the number of variants for each effect type.

        This plot shows the effect of variants on the translation of the mRNA as protein. There are three possible cases:

        • Silent: The amino acid does not change.
        • Missense: The amino acid is different.
        • Nonsense: The variant generates a stop codon.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Variant Qualities

        The line plot shows the quantity as function of the variant quality score.

        The quality score corresponds to the QUAL column of the VCF file. This score is set by the variant caller.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        166 samples had less than 1% of reads made up of overrepresented sequences

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        No samples found with any adapter contamination > 0.1%

        MultiQC v1.7 - Written by Phil Ewels, available on GitHub.

        This report uses HighCharts, jQuery, jQuery UI, Bootstrap, FileSaver.js and clipboard.js.